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Coexpression cluster:C3878: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!4.59e-90!56;UBERON:0005068!4.59e-90!56;UBERON:0006241!4.59e-90!56;UBERON:0007135!4.59e-90!56;UBERON:0000073!4.80e-82!53;UBERON:0002616!4.80e-82!53;UBERON:0001017!2.54e-74!81;UBERON:0003075!3.62e-74!82;UBERON:0007284!3.62e-74!82;UBERON:0000955!3.08e-71!68;UBERON:0006238!3.08e-71!68;UBERON:0002346!3.44e-70!86;UBERON:0001016!1.01e-68!89;UBERON:0002780!2.53e-68!41;UBERON:0001890!2.53e-68!41;UBERON:0003080!2.53e-68!41;UBERON:0006240!2.53e-68!41;UBERON:0001893!2.60e-68!34;UBERON:0003528!1.15e-67!34;UBERON:0002020!1.15e-67!34;UBERON:0001869!8.61e-63!32;UBERON:0002791!1.77e-62!32;UBERON:0003056!2.83e-59!61;UBERON:0010371!4.85e-56!104;UBERON:0007023!3.12e-53!114;UBERON:0002619!2.65e-50!22;UBERON:0010314!6.13e-48!132;UBERON:0001950!8.01e-45!20;UBERON:0000956!7.77e-44!25;UBERON:0000203!7.77e-44!25;UBERON:0004121!8.16e-39!171;UBERON:0000924!8.16e-39!171;UBERON:0006601!8.16e-39!171;UBERON:0002420!3.84e-26!9;UBERON:0007245!3.84e-26!9;UBERON:0010009!3.84e-26!9;UBERON:0010011!3.84e-26!9;UBERON:0000454!3.84e-26!9;UBERON:0000125!1.26e-25!9;UBERON:0002308!1.26e-25!9;UBERON:0011216!4.71e-24!223;UBERON:0003076!1.06e-21!15;UBERON:0003057!1.06e-21!15;UBERON:0000025!6.85e-21!192;UBERON:0009663!1.53e-20!7;UBERON:0000200!2.53e-19!6;UBERON:0002298!1.37e-17!6;UBERON:0000477!2.19e-16!373;UBERON:0001871!5.99e-16!6;UBERON:0000349!1.20e-15!5;UBERON:0004733!1.53e-14!12;UBERON:0002028!1.53e-14!12;UBERON:0007277!1.53e-14!12;UBERON:0004111!1.74e-14!240;UBERON:0000064!5.34e-14!218;UBERON:0000483!1.59e-13!306;UBERON:0004732!2.57e-13!13;UBERON:0000119!2.82e-13!309;UBERON:0000369!8.80e-13!4;UBERON:0002435!8.80e-13!4;UBERON:0000204!8.80e-13!4;UBERON:0010082!8.80e-13!4;UBERON:0000481!9.82e-11!342;UBERON:0001872!1.54e-10!5;UBERON:0002021!2.27e-10!5;UBERON:0001870!2.79e-10!3;UBERON:0005383!6.56e-10!3;UBERON:0005382!6.56e-10!3;UBERON:0001896!8.10e-10!3;UBERON:0005290!8.10e-10!3;UBERON:0010096!8.10e-10!3;UBERON:0000062!8.71e-10!503;UBERON:0002240!1.13e-09!3;UBERON:0005174!1.13e-09!3;UBERON:0001137!1.13e-09!3;UBERON:0000988!1.76e-09!3;UBERON:0001782!2.22e-09!3;UBERON:0005424!2.22e-09!3;UBERON:0000966!2.59e-08!6;UBERON:0005388!2.59e-08!6;UBERON:0001802!2.59e-08!6;UBERON:0002680!7.18e-08!9;UBERON:0001895!7.18e-08!9;UBERON:0010092!7.18e-08!9;UBERON:0002771!1.23e-07!2;UBERON:0002702!2.03e-07!2;UBERON:0000922!2.58e-07!592;UBERON:0001876!2.69e-07!2;UBERON:0001873!2.77e-07!2;UBERON:0010122!2.77e-07!2;UBERON:0001954!3.77e-07!2;UBERON:0003022!3.77e-07!2;UBERON:0002421!3.77e-07!2;UBERON:0002600!3.77e-07!2;UBERON:0005423!3.88e-07!581;UBERON:0001781!3.94e-07!4;UBERON:0001897!4.39e-07!2;UBERON:0010225!4.39e-07!2;UBERON:0002360!6.11e-07!2;UBERON:0000094!6.11e-07!2;UBERON:0010743!6.11e-07!2;UBERON:0001875!7.10e-07!2;UBERON:0006514!7.10e-07!2;UBERON:0000923!8.04e-07!560;UBERON:0010316!8.04e-07!560;UBERON:0005291!8.04e-07!560;UBERON:0006598!8.04e-07!560;UBERON:0010317!8.04e-07!560;UBERON:0002532!8.04e-07!560;UBERON:0002148!9.00e-07!2;UBERON:0006331!9.00e-07!2;UBERON:0009662!9.00e-07!2;UBERON:0000467!9.80e-07!624
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}}
}}

Revision as of 16:24, 26 November 2012


Full id: C3878_retina_temporal_amygdala_nucleus_putamen_insula_olfactory



Phase1 CAGE Peaks

Hg19::chr1:156117128..156117137,+p11@SEMA4A
Hg19::chr1:156117149..156117176,+p3@SEMA4A
Hg19::chr21:45725050..45725074,+p2@PFKL


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0006002fructose 6-phosphate metabolic process0.00871267308455652
GO:0006110regulation of glycolysis0.00871267308455652
GO:00059456-phosphofructokinase complex0.0174191905249608
GO:00038726-phosphofructokinase activity0.0174191905249608
GO:0006000fructose metabolic process0.0174191905249608
GO:0009894regulation of catabolic process0.0174191905249608
GO:0008443phosphofructokinase activity0.0174191905249608
GO:0019200carbohydrate kinase activity0.0321019727997267
GO:0006096glycolysis0.0490648290538933
GO:0006007glucose catabolic process0.0490648290538933
GO:0019320hexose catabolic process0.0490648290538933
GO:0046365monosaccharide catabolic process0.0490648290538933
GO:0046164alcohol catabolic process0.0490648290538933
GO:0044275cellular carbohydrate catabolic process0.0490648290538933
GO:0044445cytosolic part0.0490648290538933
GO:0016052carbohydrate catabolic process0.0490648290538933
GO:0006006glucose metabolic process0.0490648290538933



Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
retinal pigment epithelial cell2.22e-093
visual pigment cell3.94e-074
Uber Anatomy
Ontology termp-valuen
neural tube4.59e-9056
neural rod4.59e-9056
future spinal cord4.59e-9056
neural keel4.59e-9056
regional part of nervous system4.80e-8253
regional part of brain4.80e-8253
central nervous system2.54e-7481
neural plate3.62e-7482
presumptive neural plate3.62e-7482
brain3.08e-7168
future brain3.08e-7168
neurectoderm3.44e-7086
nervous system1.01e-6889
regional part of forebrain2.53e-6841
forebrain2.53e-6841
anterior neural tube2.53e-6841
future forebrain2.53e-6841
telencephalon2.60e-6834
brain grey matter1.15e-6734
gray matter1.15e-6734
cerebral hemisphere8.61e-6332
regional part of telencephalon1.77e-6232
pre-chordal neural plate2.83e-5961
ecto-epithelium4.85e-56104
adult organism3.12e-53114
regional part of cerebral cortex2.65e-5022
structure with developmental contribution from neural crest6.13e-48132
neocortex8.01e-4520
cerebral cortex7.77e-4425
pallium7.77e-4425
ectoderm-derived structure8.16e-39171
ectoderm8.16e-39171
presumptive ectoderm8.16e-39171
basal ganglion3.84e-269
nuclear complex of neuraxis3.84e-269
aggregate regional part of brain3.84e-269
collection of basal ganglia3.84e-269
cerebral subcortex3.84e-269
neural nucleus1.26e-259
nucleus of brain1.26e-259
organ system subdivision4.71e-24223
posterior neural tube1.06e-2115
chordal neural plate1.06e-2115
tube6.85e-21192
telencephalic nucleus1.53e-207
gyrus2.53e-196
brainstem1.37e-176
anatomical cluster2.19e-16373
temporal lobe5.99e-166
limbic system1.20e-155
segmental subdivision of hindbrain1.53e-1412
hindbrain1.53e-1412
presumptive hindbrain1.53e-1412
anatomical conduit1.74e-14240
organ part5.34e-14218
epithelium1.59e-13306
segmental subdivision of nervous system2.57e-1313
cell layer2.82e-13309
corpus striatum8.80e-134
striatum8.80e-134
ventral part of telencephalon8.80e-134
future corpus striatum8.80e-134
multi-tissue structure9.82e-11342
parietal lobe1.54e-105
occipital lobe2.27e-105
frontal cortex2.79e-103
caudate-putamen6.56e-103
dorsal striatum6.56e-103
medulla oblongata8.10e-103
myelencephalon8.10e-103
future myelencephalon8.10e-103
organ8.71e-10503
spinal cord1.13e-093
dorsal region element1.13e-093
dorsum1.13e-093
pons1.76e-093
pigmented layer of retina2.22e-093
presumptive retinal pigmented epithelium2.22e-093
retina2.59e-086
photoreceptor array2.59e-086
posterior segment of eyeball2.59e-086
regional part of metencephalon7.18e-089
metencephalon7.18e-089
future metencephalon7.18e-089
middle temporal gyrus1.23e-072
middle frontal gyrus2.03e-072
embryo2.58e-07592
amygdala2.69e-072
caudate nucleus2.77e-072
future caudate nucleus2.77e-072
Ammon's horn3.77e-072
lobe parts of cerebral cortex3.77e-072
hippocampal formation3.77e-072
limbic lobe3.77e-072
developing anatomical structure3.88e-07581
layer of retina3.94e-074
dorsal plus ventral thalamus4.39e-072
thalamic complex4.39e-072


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

No analysis results for this cluster

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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